Cycles diffuse color bake texture atlas bake is way brighter
So the reason being was the mirror modifier on the spaceship... caused a lighter tone.  Not sure why but after I removed all mirror modifiers from the scene the color stayed the same.  Thanks @Brenticus for suggesting an issue with the spaceship it lead to the fix!

Also:   I was baking into an image with the wrong color space... Whenever you generate an image for an atlas its color space is sRGB by default. I switched it to raw and that worked like a charm.  Leaving the above because somehow that did work one round.